estimate_trunclen: Automatically estimate trunclen for filtering

In alexpiper/seqateurs: Tools for trimming and processing sequence data

Automatically estimate trunclen for filtering

Description

Automatically estimate trunclen for filtering

Usage

estimate_trunclen(
  fwd,
  rev = NULL,
  threshold = 25,
  maxlength,
  minlength,
  minoverlap = 20,
  qa_sample = 5e+05,
  overlap_sample = 100,
  quiet = FALSE
)

Arguments

fwd	A path to a fastq file containing forward reads
rev	A path to a fastq file containing reverse reads
threshold	A Quality threshold used to signal the threshold to truncate the reads at
maxlength	The maximum length for the reads to be trimmed at. Suggested length of amplicon if known.
minlength	The minimum length for reads to be trimmed at to allow merging.
qa_sample	The number of reads to sample for calculating qualities.
overlap_sample	The number of reads to sample for aligning and estimating minlength
quiet	Whether progress should be printed to console

alexpiper/seqateurs documentation built on July 9, 2023, 7:21 a.m.